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Gastrointestinal Cancer NA Binary Endpoint NCT04736472

Implementing Pharmacogenetic Testing in Gastrointestinal Cancers: Complete Statistical Analysis

This record concerns a single-group implementation study of pharmacogenetic testing in gastrointestinal cancers. Its primary question is whether test results were returned before the initial dose of qualifying chemotherapy; the posted record does not report the primary endpoint result.

Trial start: 2021-03-26  ·  Enrollment: 552  ·  Sponsor: Abramson Cancer Center at Penn Medicine
Scope of this record

This page provides an independent statistical analysis and educational interpretation of publicly reported results. ClinicalTrials.gov provides the official trial registry record. Numerical trial results on this page are restricted to the results posted in the ClinicalTrials.gov record; calculations added by Clinical Biostats are labelled as such.

1. Trial at a Glance

This page covers the registry results for Implementing Pharmacogenetic Testing in Gastrointestinal Cancers (NCT04736472), a na na study. The primary outcome is Feasibility: Number and Percentage of Participants Who Had Their Pharmacogenetic Tests Returned Prior to Initial Dose.

552
Enrollment
NA
n/a
Arms
In the primary outcome
n/a
Effect
No re-analysis shown
n/a
95% CI
See limitations
FeatureRegistry value
ClinicalTrials.gov identifierNCT04736472
PhaseNA
ConditionGastrointestinal Cancer
AllocationNot applicable (single group)
Design modelSingle Group
MaskingNone (open label)
Enrollment552
Arms in the primary outcomen/a
Lead sponsorAbramson Cancer Center at Penn Medicine
Results postedYes

2. Clinical Question

Population

People with gastrointestinal cancer who had pharmacogenetic test results and began a qualifying chemotherapy are the population described for the primary feasibility measure. The registry also describes prospective, confirmatory, and BioBank cohorts. The BioBank and confirmatory cohorts are excluded from that measure because their tests were intentionally ordered after the first chemotherapy dose. Further eligibility details are not reported in the registry record.

Intervention

The study implemented pharmacogenetic testing for DPYD and UGT1A1. The record describes screening for twelve single nucleotide polymorphisms in DPYD and two in UGT1A1. Its broader implementation aim was to give cancer care providers the ability to order testing and receive results with dosing recommendations electronically.

Comparator

There was no randomized comparator. The study is described as non-randomized and single-group, with all participants undergoing genotyping. The cohorts are not identified as like-for-like treatment and control groups, so their results should not be read as a randomized comparison.

Primary question

The primary feasibility question is how many and what percentage of participants had pharmacogenetic test results returned before the first determined dose of chemotherapy. The registered timeframe is 14 days. The registry’s description limits this measure to people with both results and a qualifying chemotherapy start; it excludes the cohorts whose tests were intentionally ordered after the first dose. The endpoint result itself is not reported in the registry record.

In practical terms, this is an implementation question about the timing and availability of test results in a cancer-care workflow. It is distinct from a randomized evaluation of whether testing changes clinical outcomes. Severe treatment-related adverse events are listed as a secondary outcome, but their relationship to the primary feasibility question is not established by the information in the registry record.

3. Trial Design

This is a non-randomized, single-group implementation study of pharmacogenetic testing in gastrointestinal cancers. The registry lists allocation as NA and masking as none. It describes all participants as undergoing genotyping, rather than assignment to a testing group and a control group. Accordingly, the study does not provide a randomized comparison for estimating the effect of testing against usual care.

The record lists an enrollment of 552 and names prospective, confirmatory, and BioBank cohorts in its adverse-event information. These cohorts have different recorded event counts, but the registry does not establish them as comparable groups for treatment-effect estimation. In particular, it states that the BioBank and confirmatory cohorts are excluded from the primary feasibility measure because testing was intentionally ordered after the first chemotherapy dose.

The intervention is described as a pharmacogenetic test. The arm description specifies screening for twelve DPYD variants and two UGT1A1 variants. The study’s stated implementation goal was to make it possible for cancer care providers to order the test and receive results with dosing recommendations electronically. The detailed procedures for delivering, interpreting, and acting on results are not reported in the registry record.

The record lists the study as completed, with a start date of 2021-03-26 and primary completion on 2023-12-19. It identifies Abramson Cancer Center at Penn Medicine as sponsor and lists phase as NA. A sample-size justification, protocol-level statistical plan, and any interim-analysis plan are not reported in the registry record. Although a separate planning illustration is described using equal allocation and a two-sided significance level of 0.05, that illustration is explicitly not the trial’s own design and does not make this a two-arm randomized study.

4. Participant Flow and Accounting

The registry reports how participants moved through each stage of the study. All counts below are exactly as posted; missing counts are not inferred from other stages.

Before assignment: Of the 552 enrolled participants, 531 were eligible to begin study procedures.

Overall Study

StageProspective CohortConfirmatory CohortBioBank Control
STARTED27620235
Completed PGx Testing26820231
Completed Relevant Chemotherapy22520229
COMPLETED22520229
NOT COMPLETED5106

Reasons for not completing this period:

ReasonProspective CohortConfirmatory CohortBioBank Control
Lost to Follow-up100
Withdrawal by Subject200
Protocol Violation4806

Analysis population for the primary outcome, as defined in the registry: Number and percentage of participants with both PGx test results and who began a qualifying chemotherapy. The BioBank Cohort and Confirmatory Cohort are not included in this measure as their PGx testing was intentionally ordered after their first dose of chemotherapy, therefore how many results were returned prior to first dose was not applicable.

5. Baseline Characteristics

The table reproduces the baseline characteristics posted in the registry, which describe the participants analysed at baseline and help show whether the randomized groups were comparable.

CharacteristicUnitProspective CohortConfirmatory CohortBioBank CohortTotal
Participants analysed27620235531
Age, Categorical: <=18 yearsParticipants0000
Age, Categorical: Between 18 and 65 yearsParticipants16211149322
Age, Categorical: >=65 yearsParticipants114986209
Sex: Female, Male: FemaleParticipants12512114251
Sex: Female, Male: MaleParticipants1518121280
Ethnicity (NIH/OMB): Hispanic or LatinoParticipants90110
Ethnicity (NIH/OMB): Not Hispanic or LatinoParticipants265190284
Ethnicity (NIH/OMB): Unknown or Not ReportedParticipants21234237
Race (NIH/OMB): American Indian or Alaska NativeParticipants0000
Race (NIH/OMB): AsianParticipants110314
Race (NIH/OMB): Native Hawaiian or Other Pacific IslanderParticipants0000
Race (NIH/OMB): Black or African AmericanParticipants5003888
Race (NIH/OMB): WhiteParticipants20519189413
Race (NIH/OMB): More than one raceParticipants0000
Race (NIH/OMB): Unknown or Not ReportedParticipants101516
Region of Enrollment: United Statesparticipants27620235531
ECOG at Enrollment: 0Participants15112102265
ECOG at Enrollment: 1Participants896109204
ECOG at Enrollment: 2Participants2012142
ECOG at Enrollment: 3Participants81312
ECOG at Enrollment: NAParticipants8008

6. Primary Endpoint

The registry lists the primary outcome as Feasibility: Number and Percentage of Participants Who Had Their Pharmacogenetic Tests Returned Prior to Initial Dose, measured over 14 days.

ElementRegistry entry
Result typeCount Of Participants
Measure of spreadnot applicable
UnitParticipants
Endpoint classificationBinary Endpoint

The primary endpoint is a feasibility measure: the number and percentage of participants whose pharmacogenetic test results were returned before the first determined dose of chemotherapy. Its registered timeframe is 14 days. The measure is intended to describe whether testing can be incorporated early enough in the care process to be available before initial treatment dosing.

This endpoint addresses a practical implementation barrier identified in the study description: test turnaround and integration of results into the electronic health record. Timely results are relevant to a workflow in which providers may use pharmacogenetic information and dosing recommendations when making treatment decisions. The endpoint itself measures timing of returned results, however; it is not a direct measure of whether a recommendation was followed, whether a dose changed, or whether patient outcomes improved.

The registry defines the primary-measure population as participants with both pharmacogenetic test results and a start of qualifying chemotherapy. It excludes the BioBank and confirmatory cohorts because their testing was intentionally ordered after the first chemotherapy dose. The number and percentage observed for the endpoint are not reported in the registry record. Therefore, the stated measure explains what the study set out to assess, but the record does not establish how often the timing criterion was met.

7. Why No Re-analysis Is Shown

Reported as posted, not recalculated. Not a randomized comparison (allocation: NA); arms are not a like-for-like control comparison. A result is recalculated only when the posted data support a clean two-arm comparison, so no result is shown beyond what the sponsor posted.

8. Statistical Interpretation

Clinical Biostats interpretation

The central interpretive point is the distinction between a registered feasibility question and a reported result. The primary endpoint is clearly described as the number and percentage of participants with test results returned before the first determined dose of qualifying chemotherapy, within a stated timeframe of 14 days. The registry record does not report the endpoint’s observed count or percentage. It therefore cannot support a quantitative conclusion about the frequency of timely results.

The study’s stated purpose is implementation: investigators sought to assess whether providers could order testing and receive results with dosing recommendations electronically, with feasibility as the primary measure. That purpose should not be confused with evidence of improved treatment outcomes. The record lists severe treatment-related adverse events as a secondary outcome, but does not report a comparison that would show whether testing changed adverse-event risk. It also does not report results for the primary feasibility endpoint in the information available.

The single-group, non-randomized structure matters. Without a randomized control group, differences between the named cohorts cannot be treated as estimates of the causal effect of pharmacogenetic testing. The record explicitly cautions that the arms are not a like-for-like control comparison. Cohort counts may describe the enrolled groups, but they do not, by themselves, tell whether testing caused a change in care, treatment safety, or outcomes.

The adverse-event information should also be read descriptively. It records counts for serious and other events and deaths across the prospective, confirmatory, and BioBank cohorts, along with a list of frequently recorded serious-event terms. Those figures do not establish that the test caused or prevented events. The record does not provide the analytic comparisons, event definitions, follow-up details, or attribution methods needed to make such an inference.

In short, the registry describes an implementation study and defines a clinically relevant timing measure. It does not report the primary measure’s result in the available record. No conclusion about success or failure of implementation, or about effects on adverse events or other patient outcomes, follows from the study design description and event counts alone.

9. Statistical Methods Explained

Statistical interpretation begins with the question the design can answer. This study is described as non-randomized and single-group. Its primary question concerns the feasibility of returning pharmacogenetic results before the first determined dose of qualifying chemotherapy. The design is therefore suited to describing implementation and timing, as registered; it is not a randomized test of the effect of pharmacogenetic testing compared with a control strategy.

What does a count and percentage describe?

For a binary outcome such as meeting or not meeting a timing criterion, a count describes how many participants met the criterion, while a percentage expresses that count relative to a defined denominator. The interpretation depends on the denominator: the registry’s primary-measure description specifies participants with both test results and a qualifying chemotherapy start, while excluding the BioBank and confirmatory cohorts because their testing was ordered after the first dose. The observed count, percentage, and denominator for the primary endpoint are not reported in the registry record, so none can be inferred from the overall enrollment or adverse-event counts.

In general, a confidence interval expresses the uncertainty around an estimate under a statistical model. For a proportion, it can show how compatible a range of underlying rates is with the observed data and method. The registry record does not report a confidence interval for the primary endpoint, nor does it report the interval method. Without the endpoint estimate and its analysis details, precision cannot be assessed.

Why does the comparison structure matter?

In a randomized comparison, assignment helps make groups comparable on average, supporting an estimate of the effect of one strategy relative to another. Here, allocation is listed as NA, masking as none, and the model as single group. The registry warns that the arms are not a like-for-like control comparison. The cohort labels and their separate counts should therefore be treated as descriptions, not as randomized treatment contrasts. Differences among cohorts could reflect how they were formed or when testing was ordered; the record does not report an analysis that resolves those possibilities.

A single-group feasibility estimate can still be informative about whether a process was carried out in the studied setting, if the outcome and denominator are fully reported. But feasibility alone does not show that the implementation caused better outcomes. Nor does a test result being returned before treatment establish that the result changed a prescribing decision. Those are separate questions, and their measures and results are not reported in the registry record.

What is the role of the planning illustration?

The registry describes a sample-size planning illustration based on an observed effect, with a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation. It states that the effect to detect is a specified fraction of the observed effect. These are assumptions for a planning exercise, not the study’s own design or evidence of the study’s power. The study itself is registered as single-group and non-randomized. Any sample sizes in such an illustration are planning quantities, not observed results, and should not be interpreted as observed power.

In general, planning calculations depend on the outcome scale, target effect, variability or event rate, allocation, and testing assumptions. A calculation based on an observed effect is especially dependent on how that effect was estimated. The registry record does not report a sample-size rationale for this study, and the illustration does not substitute for a prespecified design justification. It also cannot establish whether the completed study was adequately sized for its feasibility endpoint or secondary outcomes.

How should adverse-event counts be handled?

Event counts and the number of participants recorded as affected are not necessarily interchangeable. A participant may experience more than one event, and the record’s aggregate fields do not describe how repeated events were handled. General interpretation of event rates also requires a clear denominator, event definition, observation period, and approach to attribution. The registry lists at-risk and affected counts for serious and other events by cohort, but the analytical procedures and detailed event definitions are not reported in the registry record. The listed counts therefore support descriptive reading only.

Likewise, a list of event terms and percentages is not a treatment comparison. A percentage’s interpretation depends on its denominator and counting rules, which are not given for the listed terms. The record does not report an adjusted analysis or a causal method for attributing adverse events to testing or chemotherapy. General statistical caution is particularly important when event information is presented without a randomized comparator: observed events may be clinically important to describe, but they do not isolate the effect of the implementation strategy.

What remains unknown about the analysis?

The registry lists four outcome measures and two analyses, but the available record does not identify a full analysis hierarchy, adjustment strategy, or method for handling multiple statistical tests. Multiplicity arises in general when several outcomes or tests are evaluated; without a stated plan, it is not possible to determine whether or how the chance of false-positive findings was controlled. The analysis population beyond the primary measure’s stated inclusion and exclusion description is also not reported.

Missing-data handling, the treatment of participants without returned test results, and the handling of incomplete follow-up are not reported in the registry record. These details matter because the denominator and missingness process can affect a proportion and its interpretation. The primary result itself is absent from the record, so the posted information does not permit a reanalysis or a check of reported precision. No recalculated estimate is available to compare with a sponsor analysis.

10. Multiplicity, Missing Data and Analysis Populations

The registry lists four outcome measures and two analyses. The available record does not state which outcomes were included in each analysis, identify a testing hierarchy, or describe any adjustment for multiple comparisons. In general, assessing several outcomes or tests can increase the chance of finding an apparently notable result by chance. Whether that issue applies to a particular analysis depends on the prespecified plan, which is not reported in the registry record.

The primary measure’s intended population is described: participants with both pharmacogenetic results and a qualifying chemotherapy start, excluding the BioBank and confirmatory cohorts because testing was intentionally ordered after the first dose. The record does not report the observed primary endpoint count, percentage, or analysis denominator. It also does not describe how people without returned results, those without a qualifying chemotherapy start, or other incomplete records were handled analytically.

Missing-data methods, analysis populations for secondary outcomes, and procedures for incomplete follow-up are not reported in the registry record. These omissions limit assessment of whether the reported groups and denominators would represent all enrolled participants or a selected subset. The record also does not describe imputation, sensitivity analyses, or other methods for examining the effect of missing information. No assumptions about those methods should be inferred from the study’s completion status or its stated enrollment.

11. Safety Results

The registry reports serious adverse events as affected participants divided by participants at risk.

ArmParticipants with serious adverse eventsParticipants at riskPercentage
Prospective Cohort6922530.7%
Confirmatory Cohort102050.0%
BioBank Cohort7622933.2%
Participants with at least one serious adverse event
Serious adverse events by armProspective Cohort30.7%Confirmatory Cohort50.0%BioBank Cohort33.2%% of participants with at least one serious adverse event

Deaths

ArmDeaths (participants affected of at risk)
Prospective Cohort35 of 225
Confirmatory Cohort3 of 20
BioBank Cohort47 of 229

Other (non-serious) adverse events

Participants with at least one non-serious event at or above the registry's 5% reporting threshold.

ArmParticipants affected of at risk
Prospective Cohort214 of 225
Confirmatory Cohort20 of 20
BioBank Cohort140 of 229

Most frequent serious adverse event terms

Event termOrgan systemProspective CohortConfirmatory CohortBioBank Cohort
OtherGeneral disorders17 of 2253 of 2045 of 229
VomitingGastrointestinal disorders15 of 2252 of 2019 of 229
DiarrheaGastrointestinal disorders13 of 2254 of 2016 of 229
NauseaGastrointestinal disorders14 of 2252 of 2016 of 229
PainGeneral disorders16 of 2252 of 205 of 229
SepsisInfections and infestations7 of 2251 of 2011 of 229
FeverGeneral disorders13 of 2251 of 201 of 229
NeutropeniaBlood and lymphatic system disorders8 of 2251 of 204 of 229
WeaknessGeneral disorders10 of 2250 of 200 of 229
ThrombosisBlood and lymphatic system disorders10 of 2250 of 200 of 229

Most frequent non-serious adverse event terms

Event termOrgan systemProspective CohortConfirmatory CohortBioBank Cohort
NauseaGastrointestinal disorders140 of 22515 of 2037 of 229
AnemiaBlood and lymphatic system disorders145 of 22515 of 2014 of 229
DiarrheaGastrointestinal disorders115 of 22511 of 2040 of 229
NeutropeniaBlood and lymphatic system disorders98 of 22513 of 2047 of 229
ThrombocytopeniaBlood and lymphatic system disorders91 of 2258 of 2022 of 229
VomitingGastrointestinal disorders45 of 2256 of 2022 of 229
MucositisGastrointestinal disorders35 of 2253 of 209 of 229
Hand Foot SyndromeSkin and subcutaneous tissue disorders29 of 2251 of 2017 of 229
Peripheral NeuropathyNervous system disorders0 of 2250 of 2033 of 229
DyspneaRespiratory, thoracic and mediastinal disorders29 of 2251 of 200 of 229

Serious events with the highest arm-level rate: diarrhea (20.0%), other (19.7%), vomiting (10.0%), pain (10.0%), nausea (10.0%).

Do not overextend the safety comparison. Serious-adverse-event counts are safety observations, not efficacy outcomes, and should not be combined with the primary result into a single benefit-risk number.

The adverse-event record gives descriptive counts for three cohorts. For the prospective cohort, it lists 225 at risk and 69 affected for serious events, 225 at risk and 214 affected for other events, and 35 deaths. For the confirmatory cohort, the corresponding entries are 20 at risk and 10 affected for serious events, 20 at risk and 20 affected for other events, and 3 deaths. For the BioBank cohort, the entries are 229 at risk and 76 affected for serious events, 229 at risk and 140 affected for other events, and 47 deaths.

These figures should not be interpreted as a randomized comparison or as evidence that testing caused or prevented an event. The study is single-group and the record cautions that the cohorts are not like-for-like controls. The registry also does not report the detailed event definitions, follow-up duration for these counts, attribution procedures, or whether participants with multiple events were counted once or more than once. The listed deaths are counts; a cause or relationship to the intervention is not reported in the registry record.

The serious-event terms listed include Diarrhea at 20.0%, Other at 19.7%, Vomiting at 10.0%, Pain at 10.0%, Nausea at 10.0%, and Fever at 5.8%. Their denominators and counting rules are not reported in the registry record, so these percentages should be read as listed event information rather than as directly comparable cohort risks.

12. What the Result Does, and Does Not, Mean

The record establishes the study’s implementation aim and its planned primary feasibility measure: whether results were returned before the first determined dose of qualifying chemotherapy, within a registered timeframe of 14 days. It also describes the pharmacogenetic test content and identifies severe treatment-related adverse events as a secondary outcome. These details explain what the investigators intended to assess.

The record does not report the observed result for the primary feasibility measure. Without its count, percentage, denominator, or precision estimate, the frequency of timely test-result return cannot be determined from the posted information. Study completion and an enrollment listing do not fill that gap. The registry also does not report enough analysis detail to infer how missing primary-endpoint information was handled.

Even if a feasibility result were available, the endpoint would address the timing of result availability, not by itself whether providers used the results, changed chemotherapy dosing, or improved patient outcomes. Those are related but distinct outcomes. The study’s single-group, non-randomized design also does not provide a randomized control estimate of the effects of testing. Cohort event counts and adverse-event terms are descriptive in this record and cannot establish that the test altered safety outcomes.

Accordingly, the defensible interpretation is limited: the registry describes an implementation study of pharmacogenetic testing and defines a timing-based primary question, but the available record does not give the primary answer. It does not establish whether implementation met the feasibility criterion, nor does it establish a causal effect on treatment decisions, adverse events, or patient outcomes.

13. Why This Trial Matters Statistically

This study raises a statistical question that is important in implementation research: whether a test result can be delivered in time to be useful within an existing clinical workflow. Such questions differ from asking whether a treatment improves an outcome under a randomized comparison. Measuring result timing can characterize a practical step between ordering a test and making a treatment decision.

The distinction between a process measure and a clinical outcome is central. A result returned before an initial chemotherapy dose may indicate that a workflow step occurred on time, but it does not establish that the result influenced care or changed patient outcomes. Those downstream effects require their own measures and an analysis suited to the question. The registry identifies severe treatment-related adverse events as a secondary outcome, but does not report a causal comparison or the primary feasibility result in the available record.

The design also illustrates why cohort labels should not be mistaken for control groups. The study is non-randomized and single-group, and the registry explicitly cautions that its arms are not like-for-like controls. Describing event counts by cohort is useful for context, but it does not remove differences in how the cohorts were assembled or when their testing occurred.

Finally, a precisely defined endpoint is not enough for statistical interpretation unless its observed value, denominator, uncertainty, and analysis population are reported. The registry provides the primary feasibility question and some population boundaries, but not the endpoint result or its precision. That gap limits what readers can conclude, despite the relevance of timely pharmacogenetic testing as an implementation issue.

14. Limitations

The principal limitation for interpreting this record is that the primary feasibility result is not reported. The endpoint is defined, but its observed count, percentage, denominator, and uncertainty are absent. Consequently, the record does not show how often results were returned before the initial qualifying chemotherapy dose.

The study is non-randomized and single-group, with no like-for-like control comparison. As a result, the cohort-specific adverse-event counts cannot establish the effect of testing relative to an alternative strategy. The registry does not report detailed cohort construction, further eligibility criteria, or procedures for accounting for differences among cohorts.

The registry describes the primary-measure population and its exclusion of the BioBank and confirmatory cohorts, but does not report the full analysis population or how missing test results and other incomplete records were handled. The listed timeframe is 14 days, while the endpoint description also refers to results before the first determined dose; the record does not provide additional operational details on applying that timing definition.

Adverse-event interpretation is limited by the absence of detailed event definitions, follow-up information for the listed counts, attribution methods, and counting rules for people with multiple events. Denominators and counting rules for the listed serious-event terms are not reported in the registry record. The record also does not report a multiplicity plan, statistical model for the outcomes, or the sponsor’s detailed analysis methods. These limitations restrict conclusions about both the implementation result and safety.

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18. Record Summary

NCT04736472 is a completed, non-randomized, single-group implementation study of pharmacogenetic testing in gastrointestinal cancers, sponsored by Abramson Cancer Center at Penn Medicine. The registry lists enrollment of 552, a start date of 2021-03-26, and primary completion on 2023-12-19. Masking is listed as none and phase as NA.

The test description covers twelve DPYD variants and two UGT1A1 variants. The primary feasibility measure concerns the number and percentage of participants whose results were returned before the first determined dose of qualifying chemotherapy, with a registered timeframe of 14 days. The BioBank and confirmatory cohorts are excluded from that measure because their testing was intentionally ordered after the first dose.

The registry lists severe treatment-related adverse events as a secondary outcome and includes cohort-level adverse-event counts. The primary endpoint result, detailed statistical plan, missing-data procedures, and full methods for interpreting the safety counts are not reported in the registry record.

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